Sorry, you will have to generate your final POD docs before it gets tar'ed.

One thing I'm not sure about (nor do I know if of interest to you) is whether CPAN will look at module.pod, if present, instead of module.pm

I am already generating POD using a filter I coded in Perl (and plan to share very soon). For my setup, my module.pm (or program.pl) files look like:

#!perl -w

=begin DoxPod

# Perl and DoxPod source go here

=end DoxPod

_END_
[download]

Then I can either

doxpod myModule.pm | perldoc to view,

doxpod myModule.pm >myModule.pod to make a separate POD file,

or doxpod myModule.pm | after_END_ myModule.pm to put or update the (re-) generated POD after the _END_

By using =begin and =end, "normal" POD parsers (hopefully including CPAN's information extractor) will skip the Dox-enhanced POD markup and use the generated POD